Nucleotide sequences derived from the genome of retroviruses of the HIV-1, HIV-2, and SIV type, and their uses in particular for the amplification of the genomes of these retroviruses and for the in vitro diagnosis of the diseases due to these viruses

ABSTRACT

The present invention relates to polypeptides encoded by a nucleotide sequence from an HIV-1, HIV-2, or SIV viral genome, in which the nucleotide sequence is amplified from the viral genome using a pair of primers that contain sequences that are conserved between different HIV and SIV strains. The primers are insensitive to variations in the genomes of different HIV and SIV isolates and, therefore, can be used to amplify nucleotide sequences from HIV-1, HIV-2, and SIV strains. The invention also relates to antibodies directed against these polypeptides and methods and kits for diagnosing viral infection.

This is a division of application Ser. No. 08/895,231, filed Jul. 16,1997, U.S. Pat. No. 5,786,177 which is a division of application Ser.No. 08/160,465, filed Dec. 2, 1993, U.S. Pat. No. 5,688,637 which is acontinuation of application Ser. No. 07/820,599, filed Jan. 21, 1992,now abandoned all of which are incorporated herein by reference.

The present invention relates to oligonucleotide sequences which can beused for the implementation of techniques for the amplification ofspecific nucleotide sequences of human immunodeficiency retroviruses ofthe HIV type or of monkey immunodeficiency retroviruses of the SIV type.

The invention relates in particular to the use of such sequences formethods of in vitro diagnosis in man of the infection of an individualby a retrovirus of the HIV type (at present HIV-1 and/or HIV-2).

The isolation and characterization of retroviruses grouped togetherunder the designations HIV-1 and HIV-2 were described in the Europeanpatent applications No. 85/905.513.9 and No. 87/400.151.4, respectively.These retroviruses were isolated from several patients exhibitingsymptoms of a lymphadenopathy or an Acquired Immunodeficiency Syndrome(AIDS).

The retroviruses of the HIV-2 type like the retroviruses of the HIV-1type are characterized by a tropism for the human T4 lymphocytes and bya cytopathogenic effect with regard to these lymphocytes when theymultiply within them to give rise to, among other things, generalizedand persistent polyadenopathies, or an AIDS.

Another retrovirus, designated SIV-1, this designation replacing theearlier one STLV-III, was isolated from the rhesus macaque monkey (M. D.DANIEL et al. Science, 228, 1201 (1985); N. L. LETWIN et al., Science,230, 71 (1985) under the designation “STLV-IIImac”).

Another retrovirus, designated “STLV-III_(AGM)” (or SIV_(AGM)), wasisolated from wild green monkeys. However, in contrast to the virusespresent in the rhesus macaque monkey, the presence of STLV-III_(AGM)does not appear to induce a disease of the AIDS type in the Africangreen monkey.

For reasons of semantics, these viruses will be designated in whatfollows only by the expression SIV (the expression SIV is an Englishabbreviation for “Simian Immunodeficiency Virus”, possibly followed byan abbreviation designating the species of monkey from which they arederived, for example “MAC” for “macaque” or “AGM” for the “African GreenMonkey”.

A strain of the retrovirus SIV-1lac was deposited with the C.N.C.M. onFeb. 7, 1986 under the No. I-521.

The continuation of the study of the retroviruses HIV-1 and HIV-2 hasalso led to the production of DNA sequences (cDNA) complementary to theRNAs of their genome. The complete nucleotide sequence of a cDNA of aretrovirus representative of the HIV-2 class (HIV-2 ROD) was depositedon Feb. 21, 1986 with the C.N.C.M. under the No. I-522, under thereference name LAV-2 ROD.

Similarly, the complete nucleotide sequence of a cDNA of a retrovirusrepresentative of the HIV-1 class is described by WAIN-HOBSON, SONIGO,COLE, DANOS and ALIZON in CEll (January 1985).

Also for semantic reasons, the viruses of the HIV-1 and HIV-2 type willsometimes be designated in the subsequent description by the expressionHIV.

The methods for the in vitro diagnosis of the infections by viruses ofthe HIV-1 or HIV-2 type currently practised, are based on the detectionof anti-HIV-1 or anti-HIV-2 antibodies possibly present in a biologicalsample (biopsy) or in a biological fluid, for example in a serumobtained from the patient under study, by placing this biological fluidin contact with extracts or antigens of HIV-1 or HIV-2 under conditionswhich could give rise to the production of an immunological reactionbetween these extracts or antigens and these antibodies.

There is the risk that such diagnostic methods will give rise to falsenegatives, in particular in the case of a recent infection of anindividual by the viruses of the HIV type.

The techniques of gene amplification make a considerable contribution tothe development of in vitro diagnostic methods which are particularlysensitive for viral diseases. Among these techniques of geneamplification, mention may be made of the PCR (Polymerase ChainReaction) technique as described in the European patent applications No.86/302.298.4 of Mar. 3, 1986 and No. 87/300.203.4 of Jan. 9, 1987, oralso the technique known as “Qβreplicase” described in Biotechnology,vol. 6 page 1197 (October 1988) and that which makes use of a RNApolymerase (T7RNA polymerase) described in the International patentapplication No. WO89/01050. These techniques make it possible to improvethe sensitivity of detection of the nucleic acids of the virus, andrequire the use of specific primers for synthesis.

In the case of research on the viruses of the HIV type, the choice ofprimers is problematical. In fact, owing to the great variability of thenucleotide sequences of the viral genome, a primer corresponding to theknown sequence of a given isolate of a virus of the HIV type may fail inthe amplification of certain viral variants of the HIV type.Furthermore, even if a primer is selected from a region of the genomewhich is conserved from one HIV virus to another, its “efficiency” isnot thereby insured and may give rise to poor amplification yields.

The precise objective of the present invention is to provideoligonucleotide primers which, inter alia, make possible theamplification of the genome of all viruses of the HIV and SIV types, inparticular for diagnostic purposes, with yields considered to be maximalin the present state of the art and which, in particular, do not giverise to the presence of many a specific bands.

The primers of the present invention are specific both for the virusesof the HIV-1 groups and/or the viruses of the HIV-2 and SIV groups, andare insensitive to variations of the genome of these viruses.

The object of the present invention is oligonucleotide primers of about15 to 30 nucleotides which can be used for the genomic amplification ofthe viruses of the HIV-I type and/or HIV-2 and SIV types.

The invention relates to any nucleotide sequence characterized in thatits sequence:

is either selected from those which are contained in one of thenucleotide sequences included in the gag, vpr and pol genes of theviruses HIV-1 Bru, HIV-1 Mal, HIV-1 Eli, HIV-2 ROD and SIV MAC, or inthe nef2, vif2 and vpx genes of the viruses HIV-2 ROD and SIV MAC, or inthe env, nef1, vif1 and vpr genes of the viruses HIV-1 Bru, HIV-1 Maland HIV-1 Eli, and more particularly from those which are contained inthe nucleotide sequences defined hereafter,

or (particularly in the case of the longest sequences) contains one ofthe above-mentioned nucleotide sequences derived from HIV-1 Bru or HIV-1Mal, or HIV-1 Eli or HIV-2 ROD or SIVMac, or contains a complementarynucleotide sequence of one of these latter sequences, it beingunderstood that the possible additional nucleotides which “extendbeyond” the nucleotide sequence of the type in question at the 3′ or 5′ends preferably coincide with those which are placed external to the 5′or 3′ end of the same sequence within the complete sequence of theviruses of the HIV-1, HIV-2 or SIV MAC type mentioned above,

or, if this nucleotide sequence is not identical with one of theabove-mentioned nucleotide sequences, or is not complementary to one ofthese sequences, it is nonetheless capable of hybridizing with anucleotide sequence derived from the viruses HIV-1 Bru, HIV-1 Mal, HIV-1Eli and/or with a nucleotide sequence derived from the viruses HIV-2 RODor SIV MAC mentioned above. The hybridization may be carried out at atemperature of 60° C.±1° C. (preferably 60° C.±0.5° C.), recommended foran optimal yield.

The numbering of the nucleotides mentioned below corresponds to thatused in the reference manual “Human Retrovirus and AIDS-1989” edited bythe “Los Alamos National Laboratory—New Mexico—USA”.

(The sequences of the viruses HIV-1 Mal, HIV-1 Eli were described byMONTAGNIER, SONIGO, WAIN-HOBSON and ALIZON in the European patentapplication No. 86.401380 of Jun. 23, 1986).

The sequences of the invention are synthesized in a synthesizer marketedby Applied Biosystems (phosphoro-amidite method) or in any otherapparatus employing a similar method.

The invention relates more particularly to the oligonucleotide sequencescharacterized by the following nucleotide sequences (shown in the 5′→3′sense; the initials “S” and “AS” indicate whether the oligonucleotide issense or anti-sense, i.e. whether the oligonucleotide is oriented in the5′→3′ or in the 3′→5′ sense):

1°) sequences common to the genomes of the HIV-1, HIV-2 and SIV viruses(the pairs of numbers separated by a dash indicate the position of thenucleotides in the genomes corresponding respectively to the virusesHIV-1 Bru, HIV-1 Mal, HIV-1 Eli, HIV-2 ROD and SIV):

specific sequences of the gag gene of the genome of the above-mentionedviruses (gene coding for a group of antigens specific for the nucleoidof these viruses).

Certain variants may be introduced by certain positions of thenucleotide sequences indicated below, without affecting thehybridization properties of these nucleotide sequences with the genes ofthe viruses of the HIV and/or SIV types. The nucleotide sequencescontaining these variants are shown below the original nucleotidesequences from which they are derived by substitution of one or morebases. The bases representing modifications of the initial nucleotidesequences are indicated by a letter directly beneath the base which theyreplace in the initial sequences; whereas the bases of the originalsequences which are not replaced in the sequences bearing these variantsare shown by dots.

The synthesis of the primers is carried out by using all of the variantssimultaneously. It is the mixture of all of the variants for a givensequence which is used in the tests.

MMy1: TGG CGC CCG AAC AGG GAC (SEQ ID NO:1) ... ... .T. ... ... ... (SEQID NO:2) S, 636-653, 635-652, 636-653, 859-876, 834-851 MMy2:GGC CAG GGG GAA AGA AAA A (SEQ ID NO:3) ... .C. .C. ... ... ... . (SEQID NO:4) ... ... .A. ... ... ... . (SEQ ID NO:5)S, 854-872, 864-888, 848-872, 1160-1184, 1124-1148 MMy3:TGC CCA TAC AAA ATG TTT TA (SEQ ID NO:6) ... ... C.. T.T ... ... .. (SEQID NO:7) AS, 900-881, 916-897, 900-881, 1212-1193, 1176-1157 MMy4:TGC ATG GCT GCT TGA TG (SEQ ID NO:8) ... ..A ... ..C ..G .. (SEQ IDNO:9) AS, 1385-1369, 1419-1403, 1385-1369, 1703-1687, 1667-1651 MMy4B:CTT TGC ATG GCT GCT TGA TG (SEQ ID NO:10) ..C ... ..A ... ..C ..G ..(SEQ ID NO:11) AS, 1388-1369, 1421-1403, 1388-1369, 1706-1687,    1670-1651, MMy4Ba: CAT CAA GCA GCC ATG CAA AG (SEQ ID NO:12)...C ..G ... ..T ... ..G .. (SEQ ID NO:13)S, 1369-1388, 1403-1421, 1369-1388,    1687-1706, 1651-1670, MMy28:AGG GCT GTT GGA AAT GTG G (SEQ ID NO:14) ... ... ... ... ..G ... . (SEQID NO:15) S, 2021-2039, 2055-2073, 2024-2042, 2329-2349,    2299-2318,MMy28a: CCA CAT TTC CAG CAT CCC T (SEQ ID NO:16)... ... ... ... ..G ... . (SED ID NO:17) ... ... ... ... ..C ... . (SEDID NO:18) AS, 2039-2021, 2073-2055, 2042-2024, 2349-2329,     2318-2299. specific sequences of the vpr gene: MMy18: GAT AGA TGG AAC AAG CCC CAGS, 5590-5610, 5585-5605, 5554-5574, 6233-6296,    6147-6170, MMy19:TCC ATT TCT TGC TCT CCT CTG T (SEQ ID NO:20)AS, 5870-5849, 5865-5844, 5834-5813,     6551-6531, 6454-6431,. specific sequences of the pol gene: MMy29:TAA AGC CAG GAA TGG ATG GCC CAA (SEQ ID NO:21)... ... ... ... ... ... .A. ... (SEQ ID NO:22)S, 2620-2643, 2615-2638, 2584-2607, 2971-2994,    2887-3010 MMy29a:TTG GGC CAT CCA TTC CTG GCT TTA (SEQ ID NO:23)... .T. ... ... ... ... ... ... (SEQ ID NO:24)AS, 2643-2620, 2638-2615, 2607-2584, 2994-2971     3010-2887, MMy30:TGG ACT GTC AAT GAC ATA CAG AA (SEQ ID NO:25)... ... ... ... ..T ... ... .. (SEQ ID NO:26)S, 3339-3361, 3334-3356, 3303-3325, 3690-3712,    3606-3628, MMy30a:TTC TGT ATG TCA TTG ACA GTC CA (SEQ ID NO:27)... ... ... ... ... ..T ... .. (SEQ ID NO:28)AS, 3361-3339, 3356-3334, 3325-3303, 3712-3690, 3628-3606, MMy31:CAT GGG TAC CAG CAG ACA AAG G (SEQ ID NO:29)S, 4186-4207, 4181-4202, 4150-4171, 4534-4555,    4450-4471, MMy31a:CCT TTG TGT GCT GGT ACC CAT G (SEQ ID NO:30)AS, 4207-4186, 4202-4181, 4171-4150, 4555-4534,     4471-4450, MMy32:TGG AAA GGT GAA GGG GCA GT (SEQ ID NO:31) ... ... ... ... ..A ... ..(SEQ ID NO:32) S, 4992-5011, 4987-5006, 4956-4975, 5340-5359,   5256-5275, MMy32: ACT GCC CCT TCA CCT TTC CA (SEQ ID NO:33)... ... ... ..T ... ... .. (SEQ ID NO:34) ... ... ... ..C ... ... ..(SEQ ID NO:35) AS, 5011-4992, 5006-4987, 4975-4956, 5359-5340,    5275-5256

2°) sequences common to the genomes of the HIV-2 and SIV viruses (thepairs of numbers separated by a dash indicate the position of thenucleotides in the genomes corresponding to the viruses HIV-2 ROD andSIV-MAC, respectively).

specific sequences of the nef2 gene (coding for a negative factor of 27kD)

MMy12: AGA GAC TCT TGC GGG CGC GTG (SEQ ID NO.36)S, 9165-9185, 9139-9159, (SEQ ID NO.37) MMy13:ATA TAC TTA GAA AAG GAA GAA GG (SEQ ID NO.37) S, 9542-9564, 9516-9538,MMy13bis: CCT TCT TCC TTT TCT AAG TAT AT (SEQ ID NO.38)AS, 9564-9542, 9538-9516, MMy14: AGC TGA GAC AGC AGG GAC TTT CCA (SEQ IDNO.39) AS, 9956-9933, 9893-9870, . specific sequences of the vif2 gene(coding for an infectivity factor of 23 kD) MMy20:TAT GGA GGA GGA AAA GAG ATG GAT AGT (SEQ ID NO:40)S, 5424-5450, 5340-5366, MMy21: TAG CAC TTA TTT CCC TTG CTT T (SEQ IDNO:41) S, 5754-5775, 5670-5691, MMy21bis: AAA GCA AGG GAA ATA AGT GCT A(SEQ ID NO:42) AS, 5775-5754, 5691-5670, MMy22:CCC TTG TTC ATC ATG CCA GTA T (SEQ ID NO:43) AS, 6082-6061, 5995-5974, .specific sequences of the vpx gene (coding for a protein of 12 kD)MMy23: ATG TCA GAT CCC AGG GAG A (SEQ ID NO:44) S, 5900-5918, 5813-5831,MMy24: CCT GGA GGG GGA GGA GGA GGA (SEQ ID NO:45)AS, 6228-6208, 6141-6121,

3°) Sequences common to the genomes of the viruses HIV-1 Bru, HIV-1 Maland HIV-1 Eli (the pairs of numbers separated by a dash indicate theposition of the nucleotides in the genomes corresponding to the virusesHIV-1 Bru, HIV-1 Mal and HIV-1 Eli, respectively).

specific sequences of the env gene (coding for the envelope proteins)

MMy5: CCA ATT CCC ATA CAT TAT TGT GCC CC (SEQ ID NO:46)S, 6905-6930, 6903-6928, 6860-6885 MMy5:GGG GCA CAA TAA TGT ATG GGA ATT GG (SEQ ID NO:47)AS, 6930-6905, 6928-6903, 6885-6860, MMy6:AAT GGC AGT CTA GCA GAA GAA GA (SEQ ID NO:48)S, 7055-7077, 7053-7075, 7010-7032 MMy7:ATC CTC AGG AGG GGA CCC AGA AAT T (SEQ ID NO:49)S, 7360-7384, 7349-7373, 7306-7330 MMy7a:AAT TTC TGG GTC CCC TCC TGA GGA T (SEQ ID NO:50)AS, 7384-7360, 7373-7349, 7330-7306 MMy8:GTG CTT CCT GCT GCT CCC AAG AAC CC (SEQ ID NO:51)AS, 7857-7832, 7846-7821, 7800-7775 MMy8a:GGG TTC TTG GGA GCA GCA GGA AGC AC (SEQ ID NO:52)S, 7832-7857, 7821-7846, 7775-7800, MMy9:ATG GGT GGC AAG TGG TCA AAA AGT AG (SEQ ID NO:53)... ... ... ..A ... ... ... ... .. (SEQ ID NO:68)S, 8844-8869, 8836-8861, 8787-8812, MMy9a:CTA CTT TTT GAC CAC TTG CCA CCC AT (SEQ ID NO:54)AS, 8869-8844, 8861-8836, 8812-8787, MMy78: TAT TAA CAA GAG ATG GTG G(SEQ ID NO:55) S, 7629-7647, 7612-7630, 7572-7590, MMy89:CCA GCA AGA AAA GAA TGA A (SEQ ID NO:56)S, 8224-8242, 8213-8231, 8167-8185, MMy89a: TTC ATT CTT TTC TTG CTG G(SEQ ID NO:57) AS, 8242-8224, 8231-8213, 8185-8167,. specific sequences of the nef 1 gene: MMy10:AAA AGA AAA GGG GGG ACT GGA (SEQ ID NO:58)S, 9116-9136, 9117-9137, 9062-9082, MMy10a: TCC AGT CCC CCC TTT TCT TTT(SEQ ID NO:59) AS, 9136-9116, 9137-9117, 9082-9062, MMy11:AAA GTC CCC AGC GGA AAG TCC C (SEQ ID NO:60)AS, 9503-9483, 9505-9484, 9449-9428,. specific sequences of the vif 1 gene: MMy15:GAT TAT GGA AAA CAG ATG GCA GGT GAT (SEQ ID NO:61)S, 5073-5099, 5068-5094, 5037-5063, MMy16:GCA GAC CAA CTA ATT CAT CTG TA (SEQ ID NO:62)S, 5383-5405, 5378-5400, 5347-5369, MMy16a:TAC AGA TGA ATT AGT TGG TCT GC (SEQ ID NO:63)AS, 5405-5383, 5400-5378, 5369-5347, MMy17:CTT AAG CTC CTC TAA AAG CTC TA (SEQ ID NO:64)AS, 5675-5653, 5670-5648, 5639-5617,. specific sequences of the vpu gene MMy25:GTA AGT AGT ACA TGT AAT GCA ACC T (SEQ ID NO:65)S, 6081-6105, 6076-6100, 6045-6069, MMy26:AGC AGA AGA CAG TGG CCA TGA GAG (SEQ ID NO:66)S, 6240-6263, 6238-6261, 6207-6230, MMy27:ACT ACA GAT CAT CAA TAT CCC AA (SEQ ID NO:67)AS, 6343-6321, 6338-6316, 6307-6285,

The object of the invention is also the sequences (or primers)possessing a complementary nucleotide structure to those of the primersdefined above.

It also relates to the nucleotide sequences possessing certain mutationswith respect to those defined above without the hybridizationproperties, such as defined above, of these sequences being modified.The percentage of nucleotides different from those constituting thesequences described above without thereby affecting the hybridizationproperties of the sequences of the invention may attain 40%.

Generally speaking, in the case of a sense (S) primer, a larger numberof mutations is tolerated at the 5′ end than at the 3′ end of theprimer, the 3′ end being required to hybridize perfectly with a specificstrand of a nucleotide sequence in order for this sequence to beamplified. In the case of an anti-sense (AS) primer, it is at the 3′ endthat tolerance is allowed.

The object of the invention is also the primers such as those definedabove and including a conserved stretch of at least 5 bases on eitherside of the central part which contains modifications without the abovehybridization properties being modified.

One of the characteristics of the oligonucleotide primers of theinvention is that of giving a clear-cut amplification band, usually freeof aspecific bands when the technical directions for use described inthe present invention are followed. This fact is due to the length ofthe primers which may attain 27 bases and thus increases the specificityof hybridization, as well as to the drastic conditions of use which makeit possible to eliminate parasitic combinations. In addition to thepercentage of homology with the reference matrix, the specificity foreach type of virus is a function of the length of the primer which mayattain as many as 40 bases in order to obtain an acceptable yield.

The invention also includes primers such as those described above linkedat their 5′ end to a promoter for the implementation of a method ofgenomic amplification by the synthesis of multiple copies of DNA or RNAsuch as that described in the European patent application No.88/307.102.9 of Aug. 1, 1988.

The object of the invention is in particular the use of the primersdescribed above for the implementation of a procedure of geneamplification of nucleotide sequences of the viruses of the HIV-1 and/orHIV-2 and/or SIV type, this procedure being applicable to the in vitrodiagnosis of the potential infection of an individual by a virus of theHIV-1 and/or HIV-2 type or of an animal by at least one of the threeviruses (HIV-1, HIV-2, SIV).

This method of in vitro diagnosis of the invention is carried outstarting from a biological sample (for example a biological fluid suchas serum, the lymphocytes of circulating blood) obtained from a patientunder study, and comprising mainly the following steps:

a step involving the extraction of the nucleic acid to be detectedbelonging to the genome of the virus of the HIV-1 and/or HIV-2 and/orSIV type possibly present in the above-mentioned biological sample and,where appropriate, a step involving the incubation of the said nucleicacid with a reverse transcriptase if this latter is in the form of RNAin order to obtain a double-stranded nucleic acid (this last step beingalso designated below as the step of retrotranscription of the viralRNA),

a cycle comprising the following steps:

denaturation of the double-stranded nucleic acid to be detected, whichleads to the formation of a single stranded nucleic acid,

hybridization of each of the strands of the nucleic acid obtained duringthe previous denaturation step with at least one primer according to theinvention, by placing the strands mentioned above with at least oneprimer couple according to the invention under the conditions ofhybridization defined below,

formation, starting from the primers, of the DNA complementary to thestrands to which they are hybridized in the presence of a polymerizationagent (DNA polymerase) and the four different nucleoside triphosphates(dNTP) which leads to the formation of a greater number ofdouble-stranded nucleic acids to be detected than in the previousdenaturation step, this cycle being repeated a defined number of timesin order to obtain the said nucleic acid sequence to be detectedpossibly present in the biological sample in an amount sufficient toallow its detection,

a step involving the detection of the possible presence of the nucleicacid belonging to the genome of the virus of the HIV-1 and/or HIV-2and/or SIV type in the biological sample.

The hybridization step described above is advantageously performed at60° C. for 1 minute 30 seconds in the “10×buffer”, the composition ofwhich (expressed as final concentrations for use) is indicated below.

The method of in vitro diagnosis of the invention may be carried outeither starting from the viral RNA, or from the episomal or integratedcomplementary DNA.

In fact, the genomes of the HIV and SIV viruses exist in the form of RNAor DNA, depending on the localization of the virus in the organism.

When the virus is situated within the cells of the organism, inparticular in the interior of blood cells, its RNA is recopied into DNAby a reverse transcriptase. On the other hand, the genome of the virusesof the HIV type in the extracellular medium, in particular in the blood,remains in the RNA form.

The extraction step according to the invention of the viral DNAcontained in the cells of the biological sample recommended by theinventors—in addition to the standard method usingphenol/chloroform—comprises the following steps:

suspension of the cell pellet in 0.5 ml of boiled water in a Potterhomogenizer with a wide pestle,

grinding of the cells by “forwards and backwards rotation”,

addition of Triton X100 to give a final concentration of 0.1%,

heat denaturation for 15 to 25 minutes at 100° C.,

brief centrifugation in order to remove only the cell debris,

precipitation of the DNA overnight at −20° C. by addition of 2.5 volumesof absolute ethanol and 10% of the final volume of 3 molar sodiumacetate. The DNA is subsequently recovered, then resuspended in boiledwater after having been washed twice with 70° ethanol. It should benoted that this method leads to the simultaneous precipitation of theDNAs and the RNAs which make possible the detection of the genomicmessage of the viruses of the HIV or SIV types by use of the methodcalled “direct PCR-DNA” or by that called “PCR-RNA”.

The step involving the extraction of the viral RNA is usually performedin the classical manner well-known to the person skilled in the art.

After extraction of the RNA, it is necessary to carry out an additionalstep involving the transformation of the single-stranded RNA intodouble-stranded DNA when the in vitro diagnosis of the invention isperformed on biological samples containing the viruses of the HIV-1and/or HIV-2 and/or SIV types, the genomes of which are in the RNA form.

This transformation of the RNA into DNA is carried out by treatment ofthe RNA obtained after extraction of the biological sample, inparticular serum, with a reverse transcriptase in a suitable medium.

The object of the invention more particularly among other things is amethod of in vitro diagnosis such as that defined above in which thestep of retrotranscription of viral RNA is carried out in the followingmanner:

10 μg of RNA, extracted and resuspended in water, is placed in thepresence of the primer couple at a concentration of 40 μM of each in afinal volume of 40 μl. The mixture is denatured at 100° C. for 10minutes, then plunged into ice-cold water,

10 μl of the following mixture are added: 5 μl of the “10×buffer”described below +1 unit of AMV (Avian Myeloblastosis Virus) or MuMLV(Moloney Leukemia Virus) reverse transcriptase+1 unit ofTaq-polymerase+1 μl of a 25 mM mixture of each of the 4 dNTP+water asrequired to give 10 μl. The final volume is thus 50 μl.

This reaction is carried out in two steps:

a) 1st step: synthesis of the cDNA by the action of the reversetranscriptase at 42° C. for 13 minutes,

b) 2nd step: standard gene amplification: the mixture is heated at 95°C. for 3 minutes to destroy the reverse transcriptase and to carry outthe dehybridization/hybridization step, then the cycle previouslydescribed for gene amplification is initiated.

The object of the invention is more particularly a method of in vitrodiagnosis such as that described above in which the denaturation step isperformed in the presence of one or several primer couples of theinvention. In fact, as has been specified above, one of thecharacteristics of the oligonucleotides (or primers) of the invention isthat they give a clear-cut amplification band, usually free of aspecificbands, when they are used under the following conditions:

hybridization: the primers (1 μl of a 40 μmolar (40 μM) solution of eachprimer) are placed in the presence of the matrix DNA (100 to 300 ng) forthe first step of denaturation-reassociation; the tubes containing thismixture of matrix DNA and primers is heated for 10 minutes at 100° C.,then plunged into ice-cold water in order to increase the extent ofmatrix DNA/primer reassociation. The primers must be used at a finalconcentration of 0.8 μM each in the amplification step which follows.

amplification: the 4 dNTPs are added to the preceding mixture, eachbeing used at a concentration of 0.5 μmolar in the final solution (50μl), and one unit of Taq-polymerase per 50 μl of reaction mixture; thisstep is carried out in an amplification buffer of the present invention,usually designated by the name “10×buffer”, the composition of which(when it is diluted {fraction (1/10)}) is the following: Tris-HCl, pH8.9: 50 mM; (NH₄)₂SO₄: 15 mM; MgCl₂: 5 mM; β-mercaptoethanol: 10 mM;gelatin: 0.25 mg/ml. 5 μl of this buffer and water to give 50 μl areadded to the preceding mixture.

The amplification cycles are performed in the following manner: 30 to 40cycles consisting of:

94° C. for 10 seconds (denaturation),

60° C. for 1 minute 30 (hybridization),

78° C. for 1 minute 30 (elongation).

The whole series is followed by a single cycle at 78° C. for 15 minutes.

The accuracy to ±0.3° C. of the temperatures indicated as well as theirstability during the different parts of the cycles, are essentialconditions for the production of maximal yields as well as insuring theabsence of aspecific bands.

The optimal concentration of DNA is 100 to 300 ng in the case of genomicDNA extracted from cells (of patients or in culture, mammals or otherspecies).

It is obvious that the preceding conditions represent optimal conditionsfor a final reaction mixture of 50 μl, and that these conditions may bemodified, depending on the final volume of the reaction mixture.

The use of several different primer couples (or cocktails of couples) ofthe invention makes possible either the cross-detection of several typesof the viruses of the HIV and/or SIV type, or the simultaneous detectionof several genes of a given virus of the HIV and/or SIV type.

As examples of the preferred primer couples which can be used within theframework of the present invention, mention may be made of the followingprimer couples:

MMy1-MMy4, MMy2-My4, MMy1-MMy3, MMy18-MMy19, MMy4a-MMy28a, MMy28-MMy29a,MMy29-MMy30a, MMy31-MMy32a, in particular for the in vitro diagnosis ofthe infection of an individual by HIV-1 and/or HIV-2

MMy5-MMy8, MMy6-MMy8, MMy7-MMy8, MMy5-MMy7a, MMy6-MMy7a, MMy9-MMy11,MMy10-MMy11, MMy9-MMy10a, MMy26-MMy5a, MMy8a-MMy9a, MMy8a-MMy89,MMy89a-MMy9a, MMy15-MMy17, MMy15-MMy16a, MMy16-MMy17, MMy25-MMy27,MMy26-MMy27, in particular for the in vitro diagnosis of the infectionof an individual by HIV-1,

MMy20-MMy22, MMy20-MMy21a, MMy21-MMy22, MMy23-MMy24, MMy12-MMy14,MMy12-MMy13a, for the in vitro diagnosis of the infection of anindividual by HIV-2.

The agent of polymerization used in the elongation step of the cycle isa thermostable DNA polymerase, in particular Taq polymerase, theamplifiose of the Appligene company or any thermostable DNA polymerasewhich is commercially available.

Generally speaking, the cycle of the method of in vitro diagnosis of theinvention is repeated between 30 and 40 times.

Depending on the nucleotide primer couples used, the method of in vitrodiagnosis of the invention also makes it possible to detect selectivelythe genes of the viruses of the HIV and/or SIV type present in thebiological sample.

As examples of the primer couples which can be used for theabove-mentioned method of diagnosis gene-per-gene of the invention arethe following:

MMy1-MMy4, MMy2-MMy4, MMy1-MMy3, MMy4a-MMy28a for the gag gene,

MMy18-MMy19 for the vpr gene,

MMy5-MMy8, MMy6-MMy8, MMy7-MMy8, MMy5-MMy7a, MMy6-MMy7a, MMy26-MMy5a,MMy8a-MMy9a, MMy8a-MMy89, MMy89a-MMy9a for the env gene,

MMy9-MMy11, MMy9-MMy10a, MMy10-MMy11 for the nef1 gene,

MMy15-MMy17, MMy15-MMy16a, MMy16-MMy17 for the vif1 gene,

MMy20-My22, MMy20-MMy21a, MMy21-MMy22 for the vif 2 gene,

MMy23-MMy24 for the vpx gene,

MMy12-My14, MMy12-MMy13a, MMy13-MMy14 for the nef2 gene,

MMy25-My27, MMy26-MMy27 for the vpu gene,

MMy28-MMy29a, MMy29-MMy30a, MMy30-MMy31a, MMy31-My32a for the pol gene.

However, the combinations between “S” and “AS” primers described aboveare not limiting and may be varied according to the wish of the user.

The sizes of the nucleotide fragments synthesized with the aid of theprimer couples mentioned above as examples are shown in the followingTables I to XI: (the figures indicated in the Tables below represent thenumber of nucleotides in the fragments synthesized, and the “dashes”indicate that the primer couples tested do not make it possible tocharacterize the corresponding viral strains).

TABLE I gag gag MMy1- MMy1- MMy2- MMy4.a- MMy3 MMy4 MMy4 MMy28a HIV1-BRU265 750 532 671 HIV1-MAL 282 785 556 671 HIV1-ELI 265 750 538 674HIV2-ROD 354 845 544 663 SIV 343 844 544 668

TABLE II env env MMy5- MMy5- MMy6- MMy6- MMy7a MMy8 MMy7a MMy8 HIV1-BRU480 953 330 803 HIV1-MAL 471 944 321 794 HIV1-ELI 471 941 321 791HIV2-ROD — — — — SIV — — — —

TABLE III env env MMy7-MMy8 MMy26-MMy5.a MMy8a-MMy9a HIV1-BRU 498 6911038 HIV1-MAL 498 691 1041 HIV1-ELI 495 679 1038 HIV2-ROD — — — SIV — ——

TABLE IV env env MMy8.a-MMy89 MMy89a-MMy9a HIV1-BRU 411 646 HIV1-MAL 411649 HIV1-ELI 411 646 HIV2-ROD — — SIV — —

TABLE V nef1 nef1 MMy9-My10a MMy9-MMy11 MMy10-MMy11 HIV1-BRU 293 660 388HIV1-MAL 302 660 388 HIV1-ELI 296 663 388 HIV2-ROD — — — SIV — — —

TABLE VI nef2 nef2 MMy12-MMy13a MMy12-MMy14 MMy13-MMy14 HIV1-BRU — — —HIV1-MAL — — — HIV1-ELI — — — HIV2-ROD 400 792 415 SIV 400 755 378

TABLE VII vif1 vif1 MMy15-MMy16a MMy15-MMy17 MMy16-MMy17 HIV1-BRU 333603 293 HIV1-MAL 333 603 293 HIV1-ELI 333 603 293 HIV2-ROD — — — SIV — ——

TABLE VIII vpr vif2 MMy18-MMy19 MMy20-MMy21a MMy20-MMy22 HIV1-BRU 281 —— HIV1-MAL 281 — — HIV1-ELI 281 — — HIV2-ROD 319 352 659 SIV 308 352 656

TABLE IX vif2 vpx MMy21-MMy22 MMy23-MMy24 HIV1-BRU: — — HIV1-MAL: — —HIV1-ELI: — — HIV2-ROD: 329 329 SIV : 326 329

TABLE X vpu pol MMy25-MMy27 MMy26-MMy27 MMy28-MMy29a HIV1-BRU 263 104623 HIV1-MAL 263 101 584 HIV1-ELI 263 101 584 HIV2-ROD — — 666 SIV — —712

TABLE XI pol pol MMy29-MMy30a MMy30-MMy31a MMy31-MMy32a HIV1-BRU 742 869826 HIV1-MAL 742 869 826 HIV1-ELI 742 869 826 HIV2-ROD 742 866 826 SIV742 866 826

It is to be noted that owing to their arrangement on the genome, theprimers used for amplification may be combined in a manner such thatthey can be used as probes, either after labelling with ³²p by means ofa kinase, or for use in the procedure employing cold probes to check thespecificity of the amplification band observed during an analysis by“Southern blot”. In addition to the classical combination of the primersin order that a third oligonucleotide may serve as specific internalprobe, the special case of the vif1/vpr and vif2/vpx genes due to theoverlapping of these genes, which permits cross-detection, is to benoted. Furthermore, during an analysis of the amplified DNA bysequencing, these oligonucleotides may be used as specific primes forthe DNA polymerase making possible a duplicate sequencing in each sense,hence a duplicate reading of the sequences, thus removing possibleambiguities in interpretation.

The object of the invention is also the primers such as those definedabove, labelled in particular radioactively or enzymatically, as well astheir use as nucleotide probes, in particular in the framework of themethod of in vitro diagnosis such as described above.

The object of the invention is also oligonucleotides such as thosedescribed above and containing sugars in the α-conformation. Sucholigonucleotides exhibit the property of reversing the sense of thedouble helix formed with the matrix (strand of the genome of the virus),this double helix thus passing from the “S” state to the “AS” state.

The invention also relates to the oligonucleotides described above inwhich some nucleotides are methylated and/or contain one or more sulfuratoms, in particular at the adenine residues. Such oligonucleotidespossess the property of increasing the stability of the double helix andconsequently of hybridizing better with the DNA strand to be amplified.

The invention also relates to the oligonuceotides such as thosedescribed above existing in the so-called “modified base” formcontaining nucleotides to which chromophores are covalently grafted(planar aromatic molecules such as acridine orange), in particularaccording to the method described in the article by C. Hélène publishedin “la Vie des Sciences”, compte-rendus, série générale, tome 4, No. 1,p. 17-37. Such oligonucleotides possess the property of being easilydetectable, in particular by fluorescence.

The oligonucleotides of the invention can also be used for theimplementation of a method of in vitro diagnosis of the infection ofmonkeys (macaque, mangabey monkey or green monkey) by the virus of theSIV type, this method duplicating the principal characteristics of thatdescribed above.

The object of the invention is also diagnostic kits for theimplementation of the methods of in vitro diagnosis mentioned above. Asan example, a diagnostic kit of the present invention contains:

at least one oligonucleotide primer couple according to the invention,each couple consisting of a primer which hybridizes with one of thestrands of the nucleic acid sequence to be detected, and a primer whichhybridizes with the complementary strand of this latter under theconditions defined above,

suitable reagents for the implementation of the cycle of amplificationoperations, in particular a DNA polymerase and the four differentnucleoside triphosphates, and the reaction medium designated “10×buffer”described above.

one (or more) probe which can be labelled, in particular byradioactivity, and which is capable of hybridizing specifically in thelabelled or unlabelled form with the amplified nucleic acid sequence(s)to be detected.

The invention also relates to the use of the primers of the inventionindicated above for the implementation of a procedure for the synthesisof proteins encoded in the nucleotide sequences amplified by means ofthese primers.

As an illustration, this procedure for the synthesis of proteinscomprises the amplification of the nucleotide sequences of the genomesof the viruses of the HIV or SIV type (coding for a specific proteinand, where appropriate, having undergone certain modifications of theirnucleotides) by placing in contact the said sequences with at least oneprimer couple according to the invention under the conditions describedabove, followed by the translation of these sequences thus amplifiedinto proteins; this last step is carried out in particular bytransformation of suitable host cells with the aid of vectors containingthe said amplified sequences, and the recovery of the proteins producedin these host cells.

The invention also relates to the polypeptides derived from thetranslation of the nucleotide sequences (or primers) of the invention.

The object of the invention is also the use of the anti-senseoligonucleotide primers as antiviral agents in general, in particular tocombat AIDS, as well as pharmaceutical compositions containing theseanti-sense primers in combination with a pharmaceutically acceptablevehicle.

The invention also relates to the immunogenic compositions containingone or more translation products of the nucleotide sequences accordingto the invention, and/or one or more translation products of thenucleotide sequences amplified according to the procedures describedabove starting from primers defined according to the invention, thesetranslation products being combined with a pharmaceutically acceptablevehicle.

The invention relates to the antibodies directed against one or more ofthe translation products described above (or, in other terms, capable ofgiving rise to an immunological reaction with one or more translationproducts of the nucleotide sequences according to the invention, or alsoone or more translation products of the amplified nucleotide sequencesstarting from primers defined according to the invention) and their usefor the implementation of methods of in vitro diagnosis of the infectionof an individual by a virus of the HIV-1 and/or HIV-2 type, or of ananimal by at least one of the three viruses (HIV-1, HIV-2, SIV)according to the procedures well-known to the person skilled in the art.

As an illustration, such a method of in vitro diagnosis according to theinvention comprises the placing in contact of a biological sample (inparticular serum), taken from a patient under study, with antibodiesaccording to the invention, and the detection by means of anyappropriate procedure (in particular with the aid of labelledanti-immunoglobulins) of the immunological complexes formed between theantigens of the viruses of the HIV or SIV type possibly present in thebiological sample and the said antibodies.

The object of the invention is also kits for in vitro diagnosiscontaining antibodies according to the invention and, where appropriate,suitable reagents for the detection of the immunological complex formedby reaction between the said antibodies and the antigens of the HIV orSIV viruses.

The invention also relates to a procedure for the preparation of thepolypeptides mentioned above, in particular those correspondingaccording to the universal genetic code to the nucleotide sequences (orprimers) described above, this procedure being characterized in that,starting preferably from the C-terminal amino acid, successive aminoacid residues are condensed successively one at a time in the requiredorder, or amino acid residues and fragments previously formed andalready containing several amino acid residues in the required order arecondensed, or also several fragments thus prepared beforehand arecondensed, it being understood that care will be taken to protectbeforehand all of the reactive functions borne by these amino acidresidues or fragments with the exception of the amine function of theone and the carboxyl function of the other, which normally mustparticipate in the formation of the peptide bonds, in particular afteractivation of the carboxyl function according to the known methods ofpeptide synthesis and this is continued in a stepwise manner until theN-terminal amino acid is reached.

For example, recourse may be had to the procedure of peptide synthesisin homogeneous solution described by. Houbenweyl in “Methoden derOrganischen Chemie” (Methods of Organic Chemistry) edited by W. Wunsch,vol. 15-I and II, THIEME, STUTTGART, 1974, or to that of peptidesynthesis on a solid phase described by R. D. Merrifield in “Solid PhasePeptide Synthesis” (J. Am. Chem. Soc., 45, 2149-2154).

The invention also relates to a procedure for the preparation of thenucleotide sequences (or primers) described above, this procedurecomprising the following steps:

incubation of the genomic DNA, isolated from one of the viruses of theHIV or SIV type mentioned above, with DNAase I, then addition of EDTAand purification by extraction with the mixturephenol/chloroform/isoamyl alcohol (25/24/1), then by ether,

treatment of the DNA thus extracted by Eco R1 methylase in the presenceof DTT, and purification by extraction as described above,

incubation of the DNA thus purified with the 4 deoxynucleosidetriphosphates DATP, dCTP, dGTP and dTTm in the presence of T4 DNApolymerase and DNA ligase of E.coli, then purification according to themethod described above,

the cloning of the nucleic acid thus obtained in a suitable vector andthe recovery of the desired nucleic acid with the aid of a suitableprobe.

A particularly useful procedure for the preparation of the nucleotidesequences of the invention comprises the following steps:

the synthesis of DNA by using the B-cyanoethyl phosphoramidite automatedmethod described in Bioorganic Chemistry 4, 274-325 (1986),

the cloning of the nucleic acid thus obtained in a suitable vector andthe recovery of the nucleic acid by hybridization with a suitable probe.

Another procedure for the preparation of the nucleotide sequences of theinvention comprises the following steps:

the set of chemically synthesized oligonucleotides, provided withvarious restriction sites at their ends, the sequences of which arecompatible with the sequence of amino acids of the natural polypeptideaccording to the principle described in Proc. Natl. Acad. Sci. USA, 80,7461-7465 (1983),

the cloning of the nucleic acid thus obtained in a suitable vector andthe recovery of the desired nucleic acid by hybridization with asuitable probe.

68 18 base pairs nucleic acid single linear DNA (genomic) unknown 1TGGCGCCCGA ACAGGGAC 18 18 base pairs nucleic acid single linear DNA(genomic) unknown 2 TGGCGCCTGA ACAGGGAC 18 19 base pairs nucleic acidsingle linear DNA (genomic) unknown 3 GGCCAGGGGG AAAGAAAAA 19 19 basepairs nucleic acid single linear DNA (genomic) unknown 4 GGCCCGGCGGAAAGAAAAA 19 19 base pairs nucleic acid single linear DNA (genomic)unknown 5 GGCCAGGAGG AAAGAAAAA 19 20 base pairs nucleic acid singlelinear DNA (genomic) unknown 6 TGCCCATACA AAATGTTTTA 20 20 base pairsnucleic acid single linear DNA (genomic) unknown 7 TGCCCACACT ATATGTTTTA20 17 base pairs nucleic acid single linear DNA (genomic) unknown 8TGCATGGCTG CTTGATG 17 17 base pairs nucleic acid single linear DNA(genomic) unknown 9 TGCATAGCTG CCTGGTG 17 20 base pairs nucleic acidsingle linear DNA (genomic) unknown 10 CTTTGCATGG CTGCTTGATG 20 20 basepairs nucleic acid single linear DNA (genomic) unknown 11 CTCTGCATAGCTGCCTGGTG 20 20 base pairs nucleic acid single linear DNA (genomic)unknown 12 CATCAAGCAG CCATGCAAAG 20 20 base pairs nucleic acid singlelinear DNA (genomic) unknown 13 CACCAGGCAG CTATGCAGAG 20 19 base pairsnucleic acid single linear DNA (genomic) unknown 14 AGGGCTGTTG GAAATGTGG19 19 base pairs nucleic acid single linear DNA (genomic) unknown 15AGGGCTGTTG GAAAGGTGG 19 19 base pairs nucleic acid single linear DNA(genomic) unknown 16 CCACATTTCC AGCATCCCT 19 19 base pairs nucleic acidsingle linear DNA (genomic) unknown 17 CCACATTTCC AGCAGCCCT 19 19 basepairs nucleic acid single linear DNA (genomic) unknown 18 CCACATTTCCAGCACCCCT 19 21 base pairs nucleic acid single linear DNA (genomic)unknown 19 GATAGATGGA ACAAGCCCCA G 21 22 base pairs nucleic acid singlelinear DNA (genomic) unknown 20 TCCATTTCTT GCTCTCCTCT GT 22 24 basepairs nucleic acid single linear DNA (genomic) unknown 21 TAAAGCCAGGAATGGATGGC CCAA 24 24 base pairs nucleic acid single linear DNA(genomic) unknown 22 TAAAGCCAGG AATGGATGGA CCAA 24 24 base pairs nucleicacid single linear DNA (genomic) unknown 23 TTGGGCCATC CATTCCTGGC TTTA24 24 base pairs nucleic acid single linear DNA (genomic) unknown 24TTGGTCCATC CATTCCTGGC TTTA 24 23 base pairs nucleic acid single linearDNA (genomic) unknown 25 TGGACTGTCA ATGACATACA GAA 23 23 base pairsnucleic acid single linear DNA (genomic) unknown 26 TGGACTGTCAATGATATACA GAA 23 23 base pairs nucleic acid single linear DNA (genomic)unknown 27 TTCTGTATGT CATTGACAGT CCA 23 23 base pairs nucleic acidsingle linear DNA (genomic) unknown 28 TTCTGTATGT CATTGACTGT CCA 23 22base pairs nucleic acid single linear DNA (genomic) unknown 29CATGGGTACC AGCACACAAA GG 22 22 base pairs nucleic acid single linear DNA(genomic) unknown 30 CCTTTGTGTG CTGGTACCCA TG 22 20 base pairs nucleicacid single linear DNA (genomic) unknown 31 TGGAAAGGTG AAGGGGCAGT 20 20base pairs nucleic acid single linear DNA (genomic) unknown 32TGGAAAGGTG AAGGAGCAGT 20 20 base pairs nucleic acid single linear DNA(genomic) unknown 33 ACTGCCCCTT CACCTTTCCA 20 20 base pairs nucleic acidsingle linear DNA (genomic) unknown 34 ACTGCCCCTT CTCCTTTCCA 20 20 basepairs nucleic acid single linear DNA (genomic) unknown 35 ACTGCCCCTTCCCCTTTCCA 20 21 base pairs nucleic acid single linear DNA (genomic)unknown 36 AGAGACTCTT GCGGGCGCGT G 21 23 base pairs nucleic acid singlelinear DNA (genomic) unknown 37 ATATACTTAG AAAAGGAAGA AGG 23 23 basepairs nucleic acid single linear DNA (genomic) unknown 38 CCTTCTTCCTTTTCTAAGTA TAT 23 24 base pairs nucleic acid single linear DNA (genomic)unknown 39 AGCTGAGACA GCAGGGACTT TCCA 24 27 base pairs nucleic acidsingle linear DNA (genomic) unknown 40 TATGGAGGAG GAAAAGAGAT GGATAGT 2722 base pairs nucleic acid single linear DNA (genomic) unknown 41TAGCACTTAT TTCCCTTGCT TT 22 22 base pairs nucleic acid single linear DNA(genomic) unknown 42 AAAGCAAGGG AAATAAGTGC TA 22 22 base pairs nucleicacid single linear DNA (genomic) unknown 43 CCCTTGTTCA TCATGCCAGT AT 2219 base pairs nucleic acid single linear DNA (genomic) unknown 44ATGTCAGATC CCAGGGAGA 19 21 base pairs nucleic acid single linear DNA(genomic) unknown 45 CCTGGAGGGG GAGGAGGAGG A 21 26 base pairs nucleicacid single linear DNA (genomic) unknown 46 CCAATTCCCA TACATTATTG TGCCCC26 26 base pairs nucleic acid single linear DNA (genomic) unknown 47GGGGCACAAT AATGTATGGG AATTGG 26 23 base pairs nucleic acid single linearDNA (genomic) unknown 48 AATGGCAGTC TAGCAGAAGA AGA 23 25 base pairsnucleic acid single linear DNA (genomic) unknown 49 ATCCTCAGGAGGGGACCCAG AAATT 25 25 base pairs nucleic acid single linear DNA(genomic) unknown 50 AATTTCTGGG TCCCCTCCTG AGGAT 25 26 base pairsnucleic acid single linear DNA (genomic) unknown 51 GTGCTTCCTGCTGCTCCCAA GAACCC 26 26 base pairs nucleic acid single linear DNA(genomic) unknown 52 GGGTTCTTGG GAGCAGCAGG AAGCAC 26 26 base pairsnucleic acid single linear DNA (genomic) unknown 53 ATGGGTGGCAAGTGGTCAAA AAGTAG 26 26 base pairs nucleic acid single linear DNA(genomic) unknown 54 CTACTTTTTG ACCACTTGCC ACCCAT 26 19 base pairsnucleic acid single linear DNA (genomic) unknown 55 TATTAACAAG AGATGGTGG19 19 base pairs nucleic acid single linear DNA (genomic) unknown 56CCAGCAAGAA AAGAATGAA 19 19 base pairs nucleic acid single linear DNA(genomic) unknown 57 TTCATTCTTT TCTTGCTGG 19 21 base pairs nucleic acidsingle linear DNA (genomic) unknown 58 AAAAGAAAAG GGGGGACTGG A 21 21base pairs nucleic acid single linear DNA (genomic) unknown 59TCCAGTCCCC CCTTTTCTTT T 21 22 base pairs nucleic acid single linear DNA(genomic) unknown 60 AAAGTCCCCA GCGGAAAGTC CC 22 27 base pairs nucleicacid single linear DNA (genomic) unknown 61 GATTATGGAA AACAGATGGCAGGTGAT 27 23 base pairs nucleic acid single linear DNA (genomic)unknown 62 GCAGACCAAC TAATTCATCT GTA 23 23 base pairs nucleic acidsingle linear DNA (genomic) unknown 63 TACAGATGAA TTAGTTGGTC TGC 23 23base pairs nucleic acid single linear DNA (genomic) unknown 64CTTAAGCTCC TCTAAAAGCT CTA 23 25 base pairs nucleic acid single linearDNA (genomic) unknown 65 GTAAGTAGTA CATGTAATGC AACCT 25 24 base pairsnucleic acid single linear DNA (genomic) unknown 66 AGCAGAAGACAGTGGCCATG AGAG 24 23 base pairs nucleic acid single linear DNA(genomic) unknown 67 ACTACAGATC ATCAATATCC CAA 23 26 base pairs nucleicacid single linear DNA (genomic) unknown 68 ATGGGTGGCA AATGGTCAAA AAGTAG26

What is claimed is:
 1. A polypeptide fragment of a viral protein encodedby a nucleotide sequence from a viral genome selected from the groupconsisting of HIV-1, HIV-2, and SIV and expressed by a methodcomprising: a) amplifying the nucleic acid encoding said polypeptidewith at least two primers, wherein said first primer is complementary toa region of nucleotides of the nucleic acid of said genome, said secondprimer is complementary to a region of nucleotides of the strand of DNAcomplementary to said nucleic acid of said genome, wherein said regionsof nucleotides are separated by about 100 to about 1100 base pairs whensaid complementary strands are hybridized to form one double-strandednucleic acid, and said primers are selected from the group ofnucleotides oriented in the 5′ to 3′ direction consisting of:nucleotides 636-653, 854-872, 1369-1388, and 2021-2039 of the gag geneof HIV-1 Bru; nucleotides 900-881, 1385-1369, 1388-1369, and 2039-2021of a nucleic acid sequence complementary to the gag gene of HIV-1 Bru;nucleotides 635-652, 864-888, 1403-1421, and 2055-2073 of the gag geneof HIV-1 Mal; nucleotides 916-897, 1419-1403, 1421-1403, and 2073-2055of a nucleic acid sequence complementary to the gag gene of HIV-1 Mal;nucleotides 636-653, 848-872, 1369-1388, and 2024-2042 of the gag geneof HIV-1 Eli; nucleotides 900-881, 1385-1369, 1388-1369, and 2042-2024of a nucleic acid sequence complementary the gag gene of HIV-1 Eli;nucleotides 859-876, 1160-1184, 1687-1706, and 2329-2349 of the gag geneof HIV-2 ROD; nucleotides 1212-1193, 1703-1687, 1706-1687, and 2349-2329of a nucleic acid sequence complementary to the gag gene of HIV-2 ROD;nucleotides 834-851, 1124-1148, 1651-1670, and 2299-2318 of the gag geneof SIV-MAC; nucleotides 1176-1157, 1667-1651, 1670-1651, and 2381-2299of a nucleic acid sequence complementary to the gag gene of SIV-MAC;nucleotides 5590-5610 of the vpr gene of HIV-1 Bru; nucleotides5870-5849 of a nucleic acid sequence complementary to the vpr gene ofHIV-1 Bru; nucleotides 5585-5605 of the vpr gene of HIV-1 Mal;nucleotides 5865-5844 of a nucleic acid sequence complementary to thevpr gene of HIV-1 Mal; nucleotides 5554-5574 of the vpr gene of HIV-1Eli; nucleotides 5834-5813 of a nucleic acid sequence complementary tothe vpr gene of HIV-1 Eli; nucleotides 6233-6296 of the vpr gene ofHIV-2 ROD; nucleotides 6551-6531 of a nucleic acid sequencecomplementary to the vpr gene of HIV-2 ROD; nucleotides 6147-6170 of thevpr gene of SIV-MAC; nucleotides 6454-6431 of a nucleic acid sequencecomplementary to the vpr gene of SIV-MAC; nucleotides 2620-2643,3339-3361, 4186-4207, and 4992-5011 of the pol gene of HIV-1 Bru;nucleotides 2643-2620, 3361-3339, 4207-4186, and 5011-4992 of a nucleicacid sequence complementary to the pol gene of HIV-1 Bru; nucleotides2615-2638, 3333-3356, 4181-4202, and 4987-5006 of the pol gene of HIV-1Mal; nucleotides 2638-2615, 3356-3334, 4202-4181, and 5006-4987 of anucleic acid sequence complementary to the pol gene of HIV-1 Mal;nucleotides 2584-2607, 3303-3325, 4150-4171, and 4956-4975 of the polgene of HIV-1 Eli; nucleotides 2607-2584, 3325-3303, 4171-4150, and4975-4956 of a nucleic acid sequence complementary to the pol gene ofHIV-1 Eli; nucleotides 2971-2994, 3690-3712, 4534-4555, and 5340-5359 ofthe pol gene of HIV-2 ROD; nucleotides 2994-2971, 3712-3690, 4555-4534,and 5359-5340 of a nucleic acid sequence complementary to the pol geneof HIV-2 ROD; nucleotides 2887-3010, 3606-3628, 4450-4471, and 5256-5275of the pol gene of SIV-MAC; nucleotides 3010-2887, 3628-3606, 4471-4450,and 5275-5256 of a nucleic acid sequence complementary to the pol geneof SIV-MAC; nucleotides 9165-9185 and 9542-9564 of the nef2 gene ofHIV-2 ROD; nucleotides 9564-9542 and 9956-9933 of a nucleic acidsequence complementary to the nef2 gene of HIV-2 ROD; nucleotides9139-9159 and 9516-9538 of the nef2 gene of SIV-MAC; nucleotides9538-9516 and 9893-9870 of a nucleic acid sequence complementary to thenef2 gene of SIV-MAC; nucleotides 5424-5450 and 5754-5775 of the vif2gene of HIV-2 ROD; nucleotides 5775-5754 and 6082-6061 of a nucleic acidsequence complementary to the vif2 gene of HIV-2 ROD; nucleotides5340-5366 and 5670-5691 of the vif2 gene of SIV-MAC; nucleotides5691-5670 and 5995-5974 of a nucleic acid sequence complementary to thevif2 gene of SIV-MAC; nucleotides 5900-5918 of the vpx gene of HIV-2ROD; nucleotides 6228-6208 of a nucleic acid sequence complementary tothe vpx gene of HIV-2 ROD; nucleotides 5813-5831 of the vpx gene ofSIV-MAC; nucleotides 6141-6121 of a nucleic acid sequence complementaryto the vpx gene of SIV-MAC; nucleotides 9116-9136 of the nef1 gene ofHIV-1 Bru; nucleotides 9136-9116 and 9503-9483 of a nucleic acidsequence complementary to the nef1 gene of HIV-1 Bru; nucleotides9117-9137 of the nef1 gene of HIV-1 Mal; nucleotides 9137-9117 and9505-9484 of a nucleic acid sequence complementary to the nef1 gene ofHIV-1 Mal; nucleotides 9062-9082 of the nef1 gene of HIV-1 Eli;nucleotides 9082-9062 and 9449-9428 of a nucleic acid sequencecomplementary to the nef1 gene of HIV-1 Eli; nucleotides 5073-5099 and5383-5405 of the vif1 gene of HIV-1 Bru; nucleotides 5405-5383 and5675-5653 of a nucleic acid sequence complementary to the vif1 gene ofHIV-1 Bru; nucleotides 5068-5094 and 5378-5400 of the vif1 gene of HIV-1Mal; nucleotides 5400-5378 and 5670-5648 of a nucleic acid sequencecomplementary to the vif1 gene of HIV-1 Mal; nucleotides 5037-5063 and5347-5369 of the vif1 gene of HIV-1 Eli; nucleotides 5369-5347 and5639-5617 of a nucleic acid sequence complementary to the vif1 gene ofHIV-1 Eli; nucleotides 6081-6105 and 6240-6263 of the vpu gene of HIV-1Bru; nucleotides 6343-6321 of a nucleic acid sequence complementary tothe vpu gene of HIV-1 Bru; nucleotides 6076-6100 and 6238-6261 of thevpu gene of HIV-1 Mal; nucleotides 6338-6316 of a nucleic acid sequencecomplementary to the vpu gene of HIV-1 Mal; nucleotides 6045-6069 and6207-6230 of the vpu gene of HIV-1 Eli; and nucleotides 6307-6285 of anucleic acid sequence complementary to the vpu gene of HIV-1 Eli; b)introducing said amplified nucleotide sequence into a vector; c)transforming a host cell with said vector; and d) placing saidtransformed host cell in culture and recovering said polypeptidefragment from said culture.
 2. A polypeptide fragment of a viral proteinencoded by a nucleotide sequence from a viral genome selected from thegroup consisting of HIV-1, HIV-2, and SIV and expressed by a methodcomprising: a) amplifying the nucleic acid encoding said polypeptidewith at least two primers, wherein said first primer is complementary toa region of nucleotides of the nucleic acid of said genome, said secondprimer is complementary to a region of nucleotides of the strand of DNAcomplementary to said nucleic acid of said genome, wherein said regionsof nucleotides are separated by about 100 to about 1100 base pairs whensaid complementary strands are hybridized to form one double-strandednucleic acid, and said primers are selected from the group consistingof: MMy1: TGG CGC CCG AAC AGG GAC (SEQ ID NO:1); TGG CGC CTG AAC AGG GAC(SEQ ID NO:2); MMy2: GGC CAG GGG GAA AGA AAA A (SEQ ID NO:3);GGC CCG GCG GAA AGA AAA A (SEQ ID NO:4); GGC CCG GAG GAA AGA AAA A (SEQID NO:5); MMy3: TGC CCA TAC AAA ATG TTT TA (SEQ ID NO:6);TGC CCA CAC TAT ATG TTT TA (SEQ ID NO:7); MMy4: TGC ATG GCT GCT TGA TG(SEQ ID NO:8); TGC ATA GCT GCC TGG TG (SEQ ID NO:9); MMy4B:CTT TCG ATG GCT GCT TGA TG (SEQ ID NO:10); CTC TGC ATA GCT GCT TGC TG(SEQ ID NO:11); MMy4Ba: CAT CAA GCA GCC ATG CAA AG (SEQ ID NO:12);CAC CAG GCA GCT ATG CAG AG (SEQ ID NO:13); MMy28:AGG GCT GTT GGA AAT GTG G (SEQ ID NO:14); AGG GCT GTT GGA AGT GTG G (SEQID NO:15); MMy28a: CCA CAT TTC CAG CAT CCC T (SEQ ID NO:16);CCA CAT TTC CAG CAG CCC T (SEQ ID NO:17); CCA CAT TTC CAG CAC CCC T (SEQID NO:18); MMy18: GAT AGA TGG AAC AAG CCC CAG (SEQ ID NO:19); MMy19:TCC ATT TCT TGC TCT CCT CTG T (SEQ ID NO:20); MMy29:TAA AGC CAG GAA TGG ATG GCC CAA (SEQ ID NO:21);TAA AGC CAG GAA TGG ATG GAC CAA (SEQ ID NO:22); MMy29a:TTG GGC CAT CCA TTC CTG GCT TTA (SEQ ID NO:23);TTG GTC CAT CCA TTC CTG GCT TTA (SEQ ID NO:24); MMy30:TGG ACT GTC AAT GAC ATA CAG AA (SEQ ID NO:25);TGG ACT GTC AAT GAT ATA CAG AA (SEQ ID NO:26); MMy30a:TTC TGT ATG TCA TTG ACA GTC CA (SEQ ID NO:27);TTC TGT ATG TCA TTG ACT GTC CA (SEQ ID NO:28); MMy31:CAT GGG TAC CAG CAC ACA AAG G (SEQ ID NO:29); MMy31a:CCT TTG TGT GCT GGT ACC CAT G (SEQ ID NO:30); MMy32:TGG AAA GGT GAA GGG GCA GT (SEQ ID NO:31); TGG AAA GGT GAA GGA GCA GT(SEQ ID NO:32); MMy32a: ACT GCC CCT TCA CCT TTC CA (SEQ ID NO:33);ACT GCC CCT TCT CCT TTC CA (SEQ ID NO:34); ACT GCC CCT TCC CCT TTC CA(SEQ ID NO:35); MMy12: AGA GAC TCT TGC GGG CGC GTG (SEQ ID NO:36);MMy13: ATA TAC TTA GAA AAG GAA GAA GG (SEQ ID NO:37); MMy13a:CCT TCT TCC TTT TCT AAG TAT AT (SEQ ID NO:38); MMy14:AGC TGA GAC AGC AGG GAC TTT CCA (SEQ ID NO:39); MMy20:TAT GGA GGA GGA AAA GAG ATG GAT AGT (SEQ ID NO:40); MMy21:TAG CAC TTA TTT CCC TTG CTT T (SEQ ID NO:41); MMy21a:AAA GCA AGG GAA ATA AGT GCT A (SEQ ID NO:42); MMY22:CCC TTG TTC ATC ATG CCA GTA T (SEQ ID NO:43); MMy23:ATG TCA GAT CCC AGG GAG A (SEQ ID NO:44); MMy24:CCT GGA GGG GGA GGA GGA GGA (SEQ ID NO:45); MMy10:AAA AGA AAA GGG GGG ACT GGA (SEQ ID NO:58); MMy10a:TCC AGT CCC CCC TTT TCT TTT (SEQ ID NO:59); MMy11:AAA GTC CCC AGC GGA AAG TCC C (SEQ ID NO:60); MMy15:GAT TAT GGA AAA CAG ATG GCA GGT GAT (SEQ ID NO:61); MMy16:GCA GAC CAA CTA ATT CAT CTG TA (SEQ ID NO:62); MMy16a:TAC AGA TGA ATT AGT TGG TCT GC (SEQ ID NO:63); MMy17:CTT AAG CTC CTC TAA AAG CTC TA (SEQ ID NO:64); MMy25:GTA AGT AGT ACA TGT AAT GCA ACC T (SEQ ID NO:65); MMy26:AGC AGA AGA CAG TGG CCA TGA GAG (SEQ ID NO:66); and MMy27:ACT ACA GAT CAT CAA TAT CCC AA (SEQ ID NO:67);

b) introducing said amplified nucleotide sequence into a vector; c)transforming a host cell with said vector; and d) placing saidtransformed host cell in culture and recovering said polypeptidefragment from said culture.
 3. An antibody capable of binding to thepolypeptide of claim 1 or
 2. 4. A method for the in vitro diagnosis ofthe infection of a mammal by a virus of the HIV-1, HIV-2, or SIV type,said virus comprising at least one polypeptide antigen, said methodcomprising placing a biological sample taken from said mammal in contactwith the antibody according to claim 3, and detecting the immunologicalcomplex formed between said antigen and said antibody.
 5. A kit for thediagnosis of infection of a mammal by a virus of the HIV-1, HIV-2, orSIV type, said kit comprising an antibody according to claim 3 andreagents for the detection of the immunological complex formed betweensaid antibody and said antigen.
 6. A composition comprising at least onepolypeptide according to claim 1 in combination with a pharmaceuticallyacceptable vehicle.
 7. A composition comprising at least one polypeptideaccording to claim 2 in combination with a pharmaceutically acceptablevehicle.